From 51da0002b69b0ec0c9b51cdaa3dac40ac822c865 Mon Sep 17 00:00:00 2001 From: Sebastian Urchs Date: Tue, 19 Mar 2024 13:48:13 -0400 Subject: [PATCH 01/16] =?UTF-8?q?=F0=9F=94=84=20synced=20file(s)=20with=20?= =?UTF-8?q?neurobagel/workflows=20(#697)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 🔄 synced local '.github/workflows/' with remote 'template_workflows/project_automation/' Co-authored-by: surchs --- .github/workflows/stale.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index 58641275..4e94a9bc 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -7,7 +7,7 @@ jobs: stale: runs-on: ubuntu-latest steps: - - uses: actions/stale@v9 + - uses: actions/stale@v8 with: stale-issue-message: | We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days. From bffa6cad22cb5a77d5c845a7e769eed6a301750c Mon Sep 17 00:00:00 2001 From: Sebastian Urchs Date: Thu, 21 Mar 2024 10:22:36 -0400 Subject: [PATCH 02/16] =?UTF-8?q?=F0=9F=94=84=20synced=20file(s)=20with=20?= =?UTF-8?q?neurobagel/workflows=20(#702)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 🔄 synced local '.github/workflows/' with remote 'template_workflows/project_automation/' Co-authored-by: surchs --- .github/workflows/handle_external_pr.yml | 24 ++++++++++++++++++++++++ .github/workflows/stale.yml | 2 +- 2 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/handle_external_pr.yml diff --git a/.github/workflows/handle_external_pr.yml b/.github/workflows/handle_external_pr.yml new file mode 100644 index 00000000..13c059d2 --- /dev/null +++ b/.github/workflows/handle_external_pr.yml @@ -0,0 +1,24 @@ +name: Label pull requests from forks + +on: + pull_request: + types: [opened] + +jobs: + handle_external_pr: + # Only run this entire workflow if the PR was opened from a forked repo + # The reasoning is that both bots and external contributors have to make + # a fork of the repo before they can open a PR because they don't have + # write access to the repo. + if: github.event.pull_request.head.repo.full_name != github.repository + runs-on: ubuntu-latest + env: + GH_TOKEN: ${{ secrets.NB_PROJECT_PAT }} + + steps: + - name: Add PR to project + run: | + gh pr edit ${{ github.event.pull_request.url }} --add-project Neurobagel + + - name: Label pull request with "_community" + run: gh pr edit ${{ github.event.pull_request.number }} --add-label "_community" diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index 4e94a9bc..58641275 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -7,7 +7,7 @@ jobs: stale: runs-on: ubuntu-latest steps: - - uses: actions/stale@v8 + - uses: actions/stale@v9 with: stale-issue-message: | We want to keep our issues up to date and active. This issue hasn't seen any activity in the last 75 days. From 97743b956d66b379ce0ba5b01c892b7cbcc34579 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 27 Mar 2024 10:13:20 -0400 Subject: [PATCH 03/16] Bump lint-staged from 15.2.0 to 15.2.2 (#688) Bumps [lint-staged](https://github.com/okonet/lint-staged) from 15.2.0 to 15.2.2. - [Release notes](https://github.com/okonet/lint-staged/releases) - [Changelog](https://github.com/lint-staged/lint-staged/blob/master/CHANGELOG.md) - [Commits](https://github.com/okonet/lint-staged/compare/v15.2.0...v15.2.2) --- updated-dependencies: - dependency-name: lint-staged dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- package-lock.json | 80 +++++++++++++++++------------------------------ package.json | 2 +- 2 files changed, 29 insertions(+), 53 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6bdb6125..fd011c7a 100644 --- a/package-lock.json +++ b/package-lock.json @@ -32,7 +32,7 @@ "eslint-plugin-cypress": "^2.15.1", "eslint-plugin-vue": "^9.20.1", "husky": "^8.0.3", - "lint-staged": "^15.2.0", + "lint-staged": "^15.2.2", "push-dir": "^0.4.1" } }, @@ -11018,9 +11018,9 @@ "integrity": "sha512-7ylylesZQ/PV29jhEDl3Ufjo6ZX7gCqJr5F7PKrqc93v7fzSymt1BpwEU8nAUXs8qzzvqhbjhK5QZg6Mt/HkBg==" }, "node_modules/lint-staged": { - "version": "15.2.0", - "resolved": "https://registry.npmjs.org/lint-staged/-/lint-staged-15.2.0.tgz", - "integrity": "sha512-TFZzUEV00f+2YLaVPWBWGAMq7So6yQx+GG8YRMDeOEIf95Zn5RyiLMsEiX4KTNl9vq/w+NqRJkLA1kPIo15ufQ==", + "version": "15.2.2", + "resolved": "https://registry.npmjs.org/lint-staged/-/lint-staged-15.2.2.tgz", + "integrity": "sha512-TiTt93OPh1OZOsb5B7k96A/ATl2AjIZo+vnzFZ6oHK5FuTk63ByDtxGQpHm+kFETjEWqgkF95M8FRXKR/LEBcw==", "dev": true, "dependencies": { "chalk": "5.3.0", @@ -11028,7 +11028,7 @@ "debug": "4.3.4", "execa": "8.0.1", "lilconfig": "3.0.0", - "listr2": "8.0.0", + "listr2": "8.0.1", "micromatch": "4.0.5", "pidtree": "0.6.0", "string-argv": "0.3.2", @@ -11045,13 +11045,10 @@ } }, "node_modules/lint-staged/node_modules/ansi-escapes": { - "version": "6.2.0", - "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-6.2.0.tgz", - "integrity": "sha512-kzRaCqXnpzWs+3z5ABPQiVke+iq0KXkHo8xiWV4RPTi5Yli0l97BEQuhXV1s7+aSU/fu1kUuxgS4MsQ0fRuygw==", + "version": "6.2.1", + "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-6.2.1.tgz", + "integrity": "sha512-4nJ3yixlEthEJ9Rk4vPcdBRkZvQZlYyu8j4/Mqz5sgIkddmEnH2Yj2ZrnP9S3tQOvSNRUIgVNF/1yPpRAGNRig==", "dev": true, - "dependencies": { - "type-fest": "^3.0.0" - }, "engines": { "node": ">=14.16" }, @@ -11216,9 +11213,9 @@ } }, "node_modules/lint-staged/node_modules/listr2": { - "version": "8.0.0", - "resolved": "https://registry.npmjs.org/listr2/-/listr2-8.0.0.tgz", - "integrity": "sha512-u8cusxAcyqAiQ2RhYvV7kRKNLgUvtObIbhOX2NCXqvp1UU32xIg5CT22ykS2TPKJXZWJwtK3IKLiqAGlGNE+Zg==", + "version": "8.0.1", + "resolved": "https://registry.npmjs.org/listr2/-/listr2-8.0.1.tgz", + "integrity": "sha512-ovJXBXkKGfq+CwmKTjluEqFi3p4h8xvkxGQQAQan22YCgef4KZ1mKGjzfGh6PL6AW5Csw0QiQPNuQyH+6Xk3hA==", "dev": true, "dependencies": { "cli-truncate": "^4.0.0", @@ -11411,9 +11408,9 @@ } }, "node_modules/lint-staged/node_modules/string-width": { - "version": "7.0.0", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-7.0.0.tgz", - "integrity": "sha512-GPQHj7row82Hjo9hKZieKcHIhaAIKOJvFSIZXuCU9OASVZrMNUaZuz++SPVrBjnLsnk4k+z9f2EIypgxf2vNFw==", + "version": "7.1.0", + "resolved": "https://registry.npmjs.org/string-width/-/string-width-7.1.0.tgz", + "integrity": "sha512-SEIJCWiX7Kg4c129n48aDRwLbFb2LJmXXFrWBG4NGaRtMQ3myKPKbwrD1BKqQn74oCoNMBVrfDEr5M9YxCsrkw==", "dev": true, "dependencies": { "emoji-regex": "^10.3.0", @@ -11454,18 +11451,6 @@ "url": "https://github.com/sponsors/sindresorhus" } }, - "node_modules/lint-staged/node_modules/type-fest": { - "version": "3.13.1", - "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-3.13.1.tgz", - "integrity": "sha512-tLq3bSNx+xSpwvAJnzrK0Ep5CLNWjvFTOp71URMaAEWBfRb9nnJiBoUe0tF8bI4ZFO3omgBR6NvnbzVUT3Ly4g==", - "dev": true, - "engines": { - "node": ">=14.16" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" - } - }, "node_modules/lint-staged/node_modules/wrap-ansi": { "version": "9.0.0", "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.0.tgz", @@ -27065,9 +27050,9 @@ "integrity": "sha512-7ylylesZQ/PV29jhEDl3Ufjo6ZX7gCqJr5F7PKrqc93v7fzSymt1BpwEU8nAUXs8qzzvqhbjhK5QZg6Mt/HkBg==" }, "lint-staged": { - "version": "15.2.0", - "resolved": "https://registry.npmjs.org/lint-staged/-/lint-staged-15.2.0.tgz", - "integrity": "sha512-TFZzUEV00f+2YLaVPWBWGAMq7So6yQx+GG8YRMDeOEIf95Zn5RyiLMsEiX4KTNl9vq/w+NqRJkLA1kPIo15ufQ==", + "version": "15.2.2", + "resolved": "https://registry.npmjs.org/lint-staged/-/lint-staged-15.2.2.tgz", + "integrity": "sha512-TiTt93OPh1OZOsb5B7k96A/ATl2AjIZo+vnzFZ6oHK5FuTk63ByDtxGQpHm+kFETjEWqgkF95M8FRXKR/LEBcw==", "dev": true, "requires": { "chalk": "5.3.0", @@ -27075,7 +27060,7 @@ "debug": "4.3.4", "execa": "8.0.1", "lilconfig": "3.0.0", - "listr2": "8.0.0", + "listr2": "8.0.1", "micromatch": "4.0.5", "pidtree": "0.6.0", "string-argv": "0.3.2", @@ -27083,13 +27068,10 @@ }, "dependencies": { "ansi-escapes": { - "version": "6.2.0", - "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-6.2.0.tgz", - "integrity": "sha512-kzRaCqXnpzWs+3z5ABPQiVke+iq0KXkHo8xiWV4RPTi5Yli0l97BEQuhXV1s7+aSU/fu1kUuxgS4MsQ0fRuygw==", - "dev": true, - "requires": { - "type-fest": "^3.0.0" - } + "version": "6.2.1", + "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-6.2.1.tgz", + "integrity": "sha512-4nJ3yixlEthEJ9Rk4vPcdBRkZvQZlYyu8j4/Mqz5sgIkddmEnH2Yj2ZrnP9S3tQOvSNRUIgVNF/1yPpRAGNRig==", + "dev": true }, "ansi-regex": { "version": "6.0.1", @@ -27188,9 +27170,9 @@ "dev": true }, "listr2": { - "version": "8.0.0", - "resolved": "https://registry.npmjs.org/listr2/-/listr2-8.0.0.tgz", - "integrity": "sha512-u8cusxAcyqAiQ2RhYvV7kRKNLgUvtObIbhOX2NCXqvp1UU32xIg5CT22ykS2TPKJXZWJwtK3IKLiqAGlGNE+Zg==", + "version": "8.0.1", + "resolved": "https://registry.npmjs.org/listr2/-/listr2-8.0.1.tgz", + "integrity": "sha512-ovJXBXkKGfq+CwmKTjluEqFi3p4h8xvkxGQQAQan22YCgef4KZ1mKGjzfGh6PL6AW5Csw0QiQPNuQyH+6Xk3hA==", "dev": true, "requires": { "cli-truncate": "^4.0.0", @@ -27315,9 +27297,9 @@ } }, "string-width": { - "version": "7.0.0", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-7.0.0.tgz", - "integrity": "sha512-GPQHj7row82Hjo9hKZieKcHIhaAIKOJvFSIZXuCU9OASVZrMNUaZuz++SPVrBjnLsnk4k+z9f2EIypgxf2vNFw==", + "version": "7.1.0", + "resolved": "https://registry.npmjs.org/string-width/-/string-width-7.1.0.tgz", + "integrity": "sha512-SEIJCWiX7Kg4c129n48aDRwLbFb2LJmXXFrWBG4NGaRtMQ3myKPKbwrD1BKqQn74oCoNMBVrfDEr5M9YxCsrkw==", "dev": true, "requires": { "emoji-regex": "^10.3.0", @@ -27340,12 +27322,6 @@ "integrity": "sha512-dOESqjYr96iWYylGObzd39EuNTa5VJxyvVAEm5Jnh7KGo75V43Hk1odPQkNDyXNmUR6k+gEiDVXnjB8HJ3crXw==", "dev": true }, - "type-fest": { - "version": "3.13.1", - "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-3.13.1.tgz", - "integrity": "sha512-tLq3bSNx+xSpwvAJnzrK0Ep5CLNWjvFTOp71URMaAEWBfRb9nnJiBoUe0tF8bI4ZFO3omgBR6NvnbzVUT3Ly4g==", - "dev": true - }, "wrap-ansi": { "version": "9.0.0", "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.0.tgz", diff --git a/package.json b/package.json index 58c55b18..fa8ed7c7 100644 --- a/package.json +++ b/package.json @@ -39,7 +39,7 @@ "eslint-plugin-cypress": "^2.15.1", "eslint-plugin-vue": "^9.20.1", "husky": "^8.0.3", - "lint-staged": "^15.2.0", + "lint-staged": "^15.2.2", "push-dir": "^0.4.1" } } From d4defd7188e099a0b67531ab9ea1ebee0ac38868 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 27 Mar 2024 10:37:39 -0400 Subject: [PATCH 04/16] Bump actions/setup-node from 4.0.1 to 4.0.2 (#689) Bumps [actions/setup-node](https://github.com/actions/setup-node) from 4.0.1 to 4.0.2. - [Release notes](https://github.com/actions/setup-node/releases) - [Commits](https://github.com/actions/setup-node/compare/v4.0.1...v4.0.2) --- updated-dependencies: - dependency-name: actions/setup-node dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/cd.yaml | 2 +- .github/workflows/test_e2e.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml index 5b5f80f4..f3a0d93b 100644 --- a/.github/workflows/cd.yaml +++ b/.github/workflows/cd.yaml @@ -14,7 +14,7 @@ jobs: uses: actions/checkout@v4 - name: Set up node env - uses: actions/setup-node@v4.0.1 + uses: actions/setup-node@v4.0.2 with: node-version: 18 diff --git a/.github/workflows/test_e2e.yml b/.github/workflows/test_e2e.yml index d684f240..f196ac6d 100644 --- a/.github/workflows/test_e2e.yml +++ b/.github/workflows/test_e2e.yml @@ -10,7 +10,7 @@ jobs: uses: actions/checkout@v4 - name: Set up node env - uses: actions/setup-node@v4.0.1 + uses: actions/setup-node@v4.0.2 with: node-version: 16 From 23363214c0651949feafcd56fd84fc7aa80cc550 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 27 Mar 2024 10:55:29 -0400 Subject: [PATCH 05/16] Bump husky from 8.0.3 to 9.0.11 (#691) Bumps [husky](https://github.com/typicode/husky) from 8.0.3 to 9.0.11. - [Release notes](https://github.com/typicode/husky/releases) - [Commits](https://github.com/typicode/husky/compare/v8.0.3...v9.0.11) --- updated-dependencies: - dependency-name: husky dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- package-lock.json | 18 +++++++++--------- package.json | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/package-lock.json b/package-lock.json index fd011c7a..1790fcb8 100644 --- a/package-lock.json +++ b/package-lock.json @@ -31,7 +31,7 @@ "eslint-config-airbnb": "^19.0.4", "eslint-plugin-cypress": "^2.15.1", "eslint-plugin-vue": "^9.20.1", - "husky": "^8.0.3", + "husky": "^9.0.11", "lint-staged": "^15.2.2", "push-dir": "^0.4.1" } @@ -10156,15 +10156,15 @@ } }, "node_modules/husky": { - "version": "8.0.3", - "resolved": "https://registry.npmjs.org/husky/-/husky-8.0.3.tgz", - "integrity": "sha512-+dQSyqPh4x1hlO1swXBiNb2HzTDN1I2IGLQx1GrBuiqFJfoMrnZWwVmatvSiO+Iz8fBUnf+lekwNo4c2LlXItg==", + "version": "9.0.11", + "resolved": "https://registry.npmjs.org/husky/-/husky-9.0.11.tgz", + "integrity": "sha512-AB6lFlbwwyIqMdHYhwPe+kjOC3Oc5P3nThEoW/AaO2BX3vJDjWPFxYLxokUZOo6RNX20He3AaT8sESs9NJcmEw==", "dev": true, "bin": { - "husky": "lib/bin.js" + "husky": "bin.mjs" }, "engines": { - "node": ">=14" + "node": ">=18" }, "funding": { "url": "https://github.com/sponsors/typicode" @@ -26431,9 +26431,9 @@ "integrity": "sha512-B4FFZ6q/T2jhhksgkbEW3HBvWIfDW85snkQgawt07S7J5QXTk6BkNV+0yAeZrM5QpMAdYlocGoljn0sJ/WQkFw==" }, "husky": { - "version": "8.0.3", - "resolved": "https://registry.npmjs.org/husky/-/husky-8.0.3.tgz", - "integrity": "sha512-+dQSyqPh4x1hlO1swXBiNb2HzTDN1I2IGLQx1GrBuiqFJfoMrnZWwVmatvSiO+Iz8fBUnf+lekwNo4c2LlXItg==", + "version": "9.0.11", + "resolved": "https://registry.npmjs.org/husky/-/husky-9.0.11.tgz", + "integrity": "sha512-AB6lFlbwwyIqMdHYhwPe+kjOC3Oc5P3nThEoW/AaO2BX3vJDjWPFxYLxokUZOo6RNX20He3AaT8sESs9NJcmEw==", "dev": true }, "iconv-lite": { diff --git a/package.json b/package.json index fa8ed7c7..9d95ef91 100644 --- a/package.json +++ b/package.json @@ -38,7 +38,7 @@ "eslint-config-airbnb": "^19.0.4", "eslint-plugin-cypress": "^2.15.1", "eslint-plugin-vue": "^9.20.1", - "husky": "^8.0.3", + "husky": "^9.0.11", "lint-staged": "^15.2.2", "push-dir": "^0.4.1" } From 51ba27583ec0cacc896b49f2388db42e16bd0269 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 27 Mar 2024 11:19:46 -0400 Subject: [PATCH 06/16] Bump follow-redirects from 1.15.4 to 1.15.6 (#698) Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.4 to 1.15.6. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.15.4...v1.15.6) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- package-lock.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1790fcb8..27a6e4b6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9045,9 +9045,9 @@ } }, "node_modules/follow-redirects": { - "version": "1.15.4", - "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.4.tgz", - "integrity": "sha512-Cr4D/5wlrb0z9dgERpUL3LrmPKVDsETIJhaCMeDfuFYcqa5bldGV6wBsAN6X/vxlXQtFBMrXdXxdL8CbDTGniw==", + "version": "1.15.6", + "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.6.tgz", + "integrity": "sha512-wWN62YITEaOpSK584EZXJafH1AGpO8RVgElfkuXbTOrPX4fIfOyEpW/CsiNd8JdYrAoOvafRTOEnvsO++qCqFA==", "funding": [ { "type": "individual", @@ -25624,9 +25624,9 @@ } }, "follow-redirects": { - "version": "1.15.4", - "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.4.tgz", - "integrity": "sha512-Cr4D/5wlrb0z9dgERpUL3LrmPKVDsETIJhaCMeDfuFYcqa5bldGV6wBsAN6X/vxlXQtFBMrXdXxdL8CbDTGniw==" + "version": "1.15.6", + "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.6.tgz", + "integrity": "sha512-wWN62YITEaOpSK584EZXJafH1AGpO8RVgElfkuXbTOrPX4fIfOyEpW/CsiNd8JdYrAoOvafRTOEnvsO++qCqFA==" }, "for-each": { "version": "0.3.3", From d2f791155936222cfafbb3b3cc1c826735984194 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 27 Mar 2024 23:26:03 -0400 Subject: [PATCH 07/16] Bump core-js from 3.35.0 to 3.36.1 (#707) Bumps [core-js](https://github.com/zloirock/core-js/tree/HEAD/packages/core-js) from 3.35.0 to 3.36.1. - [Release notes](https://github.com/zloirock/core-js/releases) - [Changelog](https://github.com/zloirock/core-js/blob/master/CHANGELOG.md) - [Commits](https://github.com/zloirock/core-js/commits/v3.36.1/packages/core-js) --- updated-dependencies: - dependency-name: core-js dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- package-lock.json | 14 +++++++------- package.json | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/package-lock.json b/package-lock.json index 27a6e4b6..6258e52f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -12,7 +12,7 @@ "ajv": "^8.12.0", "bootstrap": "^4.6.1", "bootstrap-vue": "^2.23.1", - "core-js": "^3.35.0", + "core-js": "^3.36.1", "file-saver": "^2.0.5", "fs": "^0.0.1-security", "nuxt": "^2.17.3", @@ -6313,9 +6313,9 @@ } }, "node_modules/core-js": { - "version": "3.35.0", - "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.35.0.tgz", - "integrity": "sha512-ntakECeqg81KqMueeGJ79Q5ZgQNR+6eaE8sxGCx62zMbAIj65q+uYvatToew3m6eAGdU4gNZwpZ34NMe4GYswg==", + "version": "3.36.1", + "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.36.1.tgz", + "integrity": "sha512-BTvUrwxVBezj5SZ3f10ImnX2oRByMxql3EimVqMysepbC9EeMUOpLwdy6Eoili2x6E4kf+ZUB5k/+Jv55alPfA==", "hasInstallScript": true, "funding": { "type": "opencollective", @@ -23548,9 +23548,9 @@ "integrity": "sha1-Z29us8OZl8LuGsOpJP1hJHSPV40=" }, "core-js": { - "version": "3.35.0", - "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.35.0.tgz", - "integrity": "sha512-ntakECeqg81KqMueeGJ79Q5ZgQNR+6eaE8sxGCx62zMbAIj65q+uYvatToew3m6eAGdU4gNZwpZ34NMe4GYswg==" + "version": "3.36.1", + "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.36.1.tgz", + "integrity": "sha512-BTvUrwxVBezj5SZ3f10ImnX2oRByMxql3EimVqMysepbC9EeMUOpLwdy6Eoili2x6E4kf+ZUB5k/+Jv55alPfA==" }, "core-js-compat": { "version": "3.35.0", diff --git a/package.json b/package.json index 9d95ef91..4c94a637 100644 --- a/package.json +++ b/package.json @@ -19,7 +19,7 @@ "ajv": "^8.12.0", "bootstrap": "^4.6.1", "bootstrap-vue": "^2.23.1", - "core-js": "^3.35.0", + "core-js": "^3.36.1", "file-saver": "^2.0.5", "fs": "^0.0.1-security", "nuxt": "^2.17.3", From 2dbf559e6f55f6f4d0572500c24ad37eee4c90da Mon Sep 17 00:00:00 2001 From: Sebastian Urchs Date: Wed, 3 Apr 2024 14:23:50 -0400 Subject: [PATCH 08/16] =?UTF-8?q?=F0=9F=94=84=20synced=20file(s)=20with=20?= =?UTF-8?q?neurobagel/workflows=20(#703)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 🔄 synced local '.github/workflows/' with remote 'template_workflows/project_automation/' * 🔄 synced local 'LICENSE' with remote 'template_configs/LICENSE' --------- Co-authored-by: surchs --- .github/workflows/handle_external_pr.yml | 12 ++++-------- LICENSE | 4 ++-- 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/.github/workflows/handle_external_pr.yml b/.github/workflows/handle_external_pr.yml index 13c059d2..0b388411 100644 --- a/.github/workflows/handle_external_pr.yml +++ b/.github/workflows/handle_external_pr.yml @@ -1,7 +1,7 @@ name: Label pull requests from forks on: - pull_request: + pull_request_target: types: [opened] jobs: @@ -12,13 +12,9 @@ jobs: # write access to the repo. if: github.event.pull_request.head.repo.full_name != github.repository runs-on: ubuntu-latest - env: - GH_TOKEN: ${{ secrets.NB_PROJECT_PAT }} steps: - - name: Add PR to project - run: | - gh pr edit ${{ github.event.pull_request.url }} --add-project Neurobagel - - name: Label pull request with "_community" - run: gh pr edit ${{ github.event.pull_request.number }} --add-label "_community" + run: gh pr edit ${{ github.event.pull_request.number }} -R ${{ github.repository }} --add-label "_community" + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/LICENSE b/LICENSE index afeaa5d5..aa94611a 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2023 Neurobagel Project, Oriagmi Lab, McGill University. +Copyright (c) 2022 - Neurobagel Project, Origami Lab, McGill University. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +SOFTWARE. \ No newline at end of file From 4ad76e738850fee1e2f9c1211801fe193462d39d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 9 Apr 2024 09:34:26 -0400 Subject: [PATCH 09/16] Bump eslint-plugin-vue from 9.20.1 to 9.24.1 (#712) Bumps [eslint-plugin-vue](https://github.com/vuejs/eslint-plugin-vue) from 9.20.1 to 9.24.1. - [Release notes](https://github.com/vuejs/eslint-plugin-vue/releases) - [Commits](https://github.com/vuejs/eslint-plugin-vue/compare/v9.20.1...v9.24.1) --- updated-dependencies: - dependency-name: eslint-plugin-vue dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- package-lock.json | 90 ++++++++++++++++++++++++++++++----------------- package.json | 2 +- 2 files changed, 59 insertions(+), 33 deletions(-) diff --git a/package-lock.json b/package-lock.json index 6258e52f..88873360 100644 --- a/package-lock.json +++ b/package-lock.json @@ -30,7 +30,7 @@ "eslint": "^8.56.0", "eslint-config-airbnb": "^19.0.4", "eslint-plugin-cypress": "^2.15.1", - "eslint-plugin-vue": "^9.20.1", + "eslint-plugin-vue": "^9.24.1", "husky": "^9.0.11", "lint-staged": "^15.2.2", "push-dir": "^0.4.1" @@ -8109,24 +8109,40 @@ } }, "node_modules/eslint-plugin-vue": { - "version": "9.20.1", - "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.20.1.tgz", - "integrity": "sha512-GyCs8K3lkEvoyC1VV97GJhP1SvqsKCiWGHnbn0gVUYiUhaH2+nB+Dv1uekv1THFMPbBfYxukrzQdltw950k+LQ==", + "version": "9.24.1", + "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.24.1.tgz", + "integrity": "sha512-wk3SuwmS1pZdcuJlokGYEi/buDOwD6KltvhIZyOnpJ/378dcQ4zchu9PAMbbLAaydCz1iYc5AozszcOOgZIIOg==", "dev": true, "dependencies": { "@eslint-community/eslint-utils": "^4.4.0", + "globals": "^13.24.0", "natural-compare": "^1.4.0", "nth-check": "^2.1.1", - "postcss-selector-parser": "^6.0.13", - "semver": "^7.5.4", - "vue-eslint-parser": "^9.4.0", + "postcss-selector-parser": "^6.0.15", + "semver": "^7.6.0", + "vue-eslint-parser": "^9.4.2", "xml-name-validator": "^4.0.0" }, "engines": { "node": "^14.17.0 || >=16.0.0" }, "peerDependencies": { - "eslint": "^6.2.0 || ^7.0.0 || ^8.0.0" + "eslint": "^6.2.0 || ^7.0.0 || ^8.0.0 || ^9.0.0" + } + }, + "node_modules/eslint-plugin-vue/node_modules/globals": { + "version": "13.24.0", + "resolved": "https://registry.npmjs.org/globals/-/globals-13.24.0.tgz", + "integrity": "sha512-AhO5QUcj8llrbG09iWhPU2B204J1xnPeL8kQmVorSsy+Sjj1sk8gIyh6cUocGmH4L0UuhAJy+hJMRA4mgA4mFQ==", + "dev": true, + "dependencies": { + "type-fest": "^0.20.2" + }, + "engines": { + "node": ">=8" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" } }, "node_modules/eslint-plugin-vue/node_modules/lru-cache": { @@ -8142,9 +8158,9 @@ } }, "node_modules/eslint-plugin-vue/node_modules/semver": { - "version": "7.5.4", - "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz", - "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==", + "version": "7.6.0", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.0.tgz", + "integrity": "sha512-EnwXhrlwXMk9gKu5/flx5sv/an57AkRplG3hTK68W7FRDN+k+OWBj65M7719OkA82XLBxrcX0KSHj+X5COhOVg==", "dev": true, "dependencies": { "lru-cache": "^6.0.0" @@ -17791,9 +17807,9 @@ "integrity": "sha512-vKl1skEKn8EK9f8P2ZzhRnuaRHLHrlt1sbRmazlvsx6EiC3A8oWF8YCBrMJzoN+W3OnElwIGbVjsx6/xelY1AA==" }, "node_modules/vue-eslint-parser": { - "version": "9.4.0", - "resolved": "https://registry.npmjs.org/vue-eslint-parser/-/vue-eslint-parser-9.4.0.tgz", - "integrity": "sha512-7KsNBb6gHFA75BtneJsoK/dbZ281whUIwFYdQxA68QrCrGMXYzUMbPDHGcOQ0OocIVKrWSKWXZ4mL7tonCXoUw==", + "version": "9.4.2", + "resolved": "https://registry.npmjs.org/vue-eslint-parser/-/vue-eslint-parser-9.4.2.tgz", + "integrity": "sha512-Ry9oiGmCAK91HrKMtCrKFWmSFWvYkpGglCeFAIqDdr9zdXmMMpJOmUJS7WWsW7fX81h6mwHmUZCQQ1E0PkSwYQ==", "dev": true, "dependencies": { "debug": "^4.3.4", @@ -17852,9 +17868,9 @@ } }, "node_modules/vue-eslint-parser/node_modules/semver": { - "version": "7.5.4", - "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz", - "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==", + "version": "7.6.0", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.0.tgz", + "integrity": "sha512-EnwXhrlwXMk9gKu5/flx5sv/an57AkRplG3hTK68W7FRDN+k+OWBj65M7719OkA82XLBxrcX0KSHj+X5COhOVg==", "dev": true, "dependencies": { "lru-cache": "^6.0.0" @@ -25013,20 +25029,30 @@ "requires": {} }, "eslint-plugin-vue": { - "version": "9.20.1", - "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.20.1.tgz", - "integrity": "sha512-GyCs8K3lkEvoyC1VV97GJhP1SvqsKCiWGHnbn0gVUYiUhaH2+nB+Dv1uekv1THFMPbBfYxukrzQdltw950k+LQ==", + "version": "9.24.1", + "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.24.1.tgz", + "integrity": "sha512-wk3SuwmS1pZdcuJlokGYEi/buDOwD6KltvhIZyOnpJ/378dcQ4zchu9PAMbbLAaydCz1iYc5AozszcOOgZIIOg==", "dev": true, "requires": { "@eslint-community/eslint-utils": "^4.4.0", + "globals": "^13.24.0", "natural-compare": "^1.4.0", "nth-check": "^2.1.1", - "postcss-selector-parser": "^6.0.13", - "semver": "^7.5.4", - "vue-eslint-parser": "^9.4.0", + "postcss-selector-parser": "^6.0.15", + "semver": "^7.6.0", + "vue-eslint-parser": "^9.4.2", "xml-name-validator": "^4.0.0" }, "dependencies": { + "globals": { + "version": "13.24.0", + "resolved": "https://registry.npmjs.org/globals/-/globals-13.24.0.tgz", + "integrity": "sha512-AhO5QUcj8llrbG09iWhPU2B204J1xnPeL8kQmVorSsy+Sjj1sk8gIyh6cUocGmH4L0UuhAJy+hJMRA4mgA4mFQ==", + "dev": true, + "requires": { + "type-fest": "^0.20.2" + } + }, "lru-cache": { "version": "6.0.0", "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-6.0.0.tgz", @@ -25037,9 +25063,9 @@ } }, "semver": { - "version": "7.5.4", - "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz", - "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==", + "version": "7.6.0", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.0.tgz", + "integrity": "sha512-EnwXhrlwXMk9gKu5/flx5sv/an57AkRplG3hTK68W7FRDN+k+OWBj65M7719OkA82XLBxrcX0KSHj+X5COhOVg==", "dev": true, "requires": { "lru-cache": "^6.0.0" @@ -31816,9 +31842,9 @@ "integrity": "sha512-vKl1skEKn8EK9f8P2ZzhRnuaRHLHrlt1sbRmazlvsx6EiC3A8oWF8YCBrMJzoN+W3OnElwIGbVjsx6/xelY1AA==" }, "vue-eslint-parser": { - "version": "9.4.0", - "resolved": "https://registry.npmjs.org/vue-eslint-parser/-/vue-eslint-parser-9.4.0.tgz", - "integrity": "sha512-7KsNBb6gHFA75BtneJsoK/dbZ281whUIwFYdQxA68QrCrGMXYzUMbPDHGcOQ0OocIVKrWSKWXZ4mL7tonCXoUw==", + "version": "9.4.2", + "resolved": "https://registry.npmjs.org/vue-eslint-parser/-/vue-eslint-parser-9.4.2.tgz", + "integrity": "sha512-Ry9oiGmCAK91HrKMtCrKFWmSFWvYkpGglCeFAIqDdr9zdXmMMpJOmUJS7WWsW7fX81h6mwHmUZCQQ1E0PkSwYQ==", "dev": true, "requires": { "debug": "^4.3.4", @@ -31856,9 +31882,9 @@ } }, "semver": { - "version": "7.5.4", - "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz", - "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==", + "version": "7.6.0", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.0.tgz", + "integrity": "sha512-EnwXhrlwXMk9gKu5/flx5sv/an57AkRplG3hTK68W7FRDN+k+OWBj65M7719OkA82XLBxrcX0KSHj+X5COhOVg==", "dev": true, "requires": { "lru-cache": "^6.0.0" diff --git a/package.json b/package.json index 4c94a637..99aa5910 100644 --- a/package.json +++ b/package.json @@ -37,7 +37,7 @@ "eslint": "^8.56.0", "eslint-config-airbnb": "^19.0.4", "eslint-plugin-cypress": "^2.15.1", - "eslint-plugin-vue": "^9.20.1", + "eslint-plugin-vue": "^9.24.1", "husky": "^9.0.11", "lint-staged": "^15.2.2", "push-dir": "^0.4.1" From 9b5ffcfba1b535eb966ec30b305c04a4d608b98a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 13 Apr 2024 10:38:45 -0400 Subject: [PATCH 10/16] Bump tar from 6.2.0 to 6.2.1 (#716) Bumps [tar](https://github.com/isaacs/node-tar) from 6.2.0 to 6.2.1. - [Release notes](https://github.com/isaacs/node-tar/releases) - [Changelog](https://github.com/isaacs/node-tar/blob/main/CHANGELOG.md) - [Commits](https://github.com/isaacs/node-tar/compare/v6.2.0...v6.2.1) --- updated-dependencies: - dependency-name: tar dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- package-lock.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/package-lock.json b/package-lock.json index 88873360..fe9e8f78 100644 --- a/package-lock.json +++ b/package-lock.json @@ -16687,9 +16687,9 @@ } }, "node_modules/tar": { - "version": "6.2.0", - "resolved": "https://registry.npmjs.org/tar/-/tar-6.2.0.tgz", - "integrity": "sha512-/Wo7DcT0u5HUV486xg675HtjNd3BXZ6xDbzsCUZPt5iw8bTQ63bP0Raut3mvro9u+CUyq7YQd8Cx55fsZXxqLQ==", + "version": "6.2.1", + "resolved": "https://registry.npmjs.org/tar/-/tar-6.2.1.tgz", + "integrity": "sha512-DZ4yORTwrbTj/7MZYq2w+/ZFdI6OZ/f9SFHR+71gIVUZhOQPHzVCLpvRnPgyaMpfWxxk/4ONva3GQSyNIKRv6A==", "dependencies": { "chownr": "^2.0.0", "fs-minipass": "^2.0.0", @@ -31013,9 +31013,9 @@ "integrity": "sha512-4WK/bYZmj8xLr+HUCODHGF1ZFzsYffasLUgEiMBY4fgtltdO6B4WJtlSbPaDTLpYTcGVwM2qLnFTICEcNxs3kA==" }, "tar": { - "version": "6.2.0", - "resolved": "https://registry.npmjs.org/tar/-/tar-6.2.0.tgz", - "integrity": "sha512-/Wo7DcT0u5HUV486xg675HtjNd3BXZ6xDbzsCUZPt5iw8bTQ63bP0Raut3mvro9u+CUyq7YQd8Cx55fsZXxqLQ==", + "version": "6.2.1", + "resolved": "https://registry.npmjs.org/tar/-/tar-6.2.1.tgz", + "integrity": "sha512-DZ4yORTwrbTj/7MZYq2w+/ZFdI6OZ/f9SFHR+71gIVUZhOQPHzVCLpvRnPgyaMpfWxxk/4ONva3GQSyNIKRv6A==", "requires": { "chownr": "^2.0.0", "fs-minipass": "^2.0.0", From e335b03a3a8e1d3a7080caa95571c72df49a6766 Mon Sep 17 00:00:00 2001 From: Sebastian Urchs Date: Mon, 15 Apr 2024 16:31:03 -0400 Subject: [PATCH 11/16] [FIX] Remove existing annotations from data dictionaries (#715) * Add a warning about limitations for data dictionary * Remove annotations This step does not have a test because the corresponding store method never received one ... * Update pages/home.vue Co-authored-by: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com> * [FIX] Missed updates --------- Co-authored-by: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com> --- components/annot-explanation.vue | 8 +++++--- components/tool-navbar.vue | 4 +++- cypress/component/home_page.cy.js | 12 ++++++++++++ cypress/e2e/page/index-pagetests.cy.js | 22 ++++++++++++++++++++++ pages/home.vue | 21 ++++++++++++++++++--- store/index.js | 10 +++++++--- 6 files changed, 67 insertions(+), 10 deletions(-) diff --git a/components/annot-explanation.vue b/components/annot-explanation.vue index abe54b41..36a2e384 100644 --- a/components/annot-explanation.vue +++ b/components/annot-explanation.vue @@ -7,11 +7,13 @@ {{ uiText.cardTitle }} -
    -
  • + +
      +
    • {{ sentence }}.
      • -
    +
+ diff --git a/components/tool-navbar.vue b/components/tool-navbar.vue index 11502d8e..fb0dc070 100644 --- a/components/tool-navbar.vue +++ b/components/tool-navbar.vue @@ -13,7 +13,9 @@ alt="Neurobagel Logo" class="nav-logo" />
- {{ uiText.toolName }} beta + {{ uiText.toolName }} + beta +

diff --git a/cypress/component/home_page.cy.js b/cypress/component/home_page.cy.js index 5fc0bc39..b56caa59 100644 --- a/cypress/component/home_page.cy.js +++ b/cypress/component/home_page.cy.js @@ -41,6 +41,17 @@ describe("The Home page", () => { cy.get("[data-cy='data-dictionary-selector']").should("be.visible").contains("Choose file"); }); + it("Shows a warning about not being able to reuse annotations in the data dictionary", () => { + cy.mount(homePage, { + + mocks: { $store: store }, + stubs: stubs, + plugins: ["bootstrap-vue"] + }); + + cy.get("[data-cy='cannot-reuse-annotations-button']").should('be.visible').contains("Cannot reuse annotations"); + }); + it("Correctly displays previews of the loaded data", () => { // Act @@ -136,4 +147,5 @@ describe("The Home page", () => { }); cy.get("[data-cy='data-dictionary-selector']").contains("example_short.json"); }); + }); diff --git a/cypress/e2e/page/index-pagetests.cy.js b/cypress/e2e/page/index-pagetests.cy.js index bff5ebf5..27060253 100644 --- a/cypress/e2e/page/index-pagetests.cy.js +++ b/cypress/e2e/page/index-pagetests.cy.js @@ -92,6 +92,28 @@ describe("Tests on the index page via store interaction", () => { // 3. Assert that categorization nav item and next button are *still* enabled cy.assertNextPageAccess("categorization", true); }); + + it("A big red warning is shown next to the data dictionary button to say: can't use Annotations", () => { + + // 1. Assert that categorization nav item and next button are disabled + cy.assertNextPageAccess("categorization", false); + + // 2. Select data table file + cy.get("[data-cy='data-table-selector']") + .contains("Choose file") + .selectFile(dataFolder + p_dataset.data_table); + + // 3. Assert that categorization nav item and next button are enabled + cy.assertNextPageAccess("categorization", true); + + // 4. Select participants dictionary + cy.get("[data-cy='data-dictionary-selector']") + .contains("Choose file") + .selectFile(dataFolder + p_dataset.data_dictionary); + + // 3. Assert that categorization nav item and next button are *still* enabled + cy.assertNextPageAccess("categorization", true); + }); }); }); }); \ No newline at end of file diff --git a/pages/home.vue b/pages/home.vue index 7ac98f4c..e8cec2ab 100644 --- a/pages/home.vue +++ b/pages/home.vue @@ -17,7 +17,9 @@ 🏗️ This tool (like all of neurobagel) is under active development and we welcome any feedback or suggestions. Feel free to use our feedback widget on the side of the page.

- Summary of annotation steps + + Summary of annotation steps +

@@ -27,14 +29,15 @@

  • Upload a TSV phenotypic file (see our docs for the TSV requirements)
  • Upload a BIDS-compatible JSON data dictionary (optional)
  • Annotate any or all COLUMNS in your data table by telling us what kind of subject information they are "about"
    • -
  • Annotate the unique VALUES in the columns you have annotated, by mapping them to controlled terms from +
  • + Annotate the unique VALUES in the columns you have annotated, by mapping them to controlled terms from existing vocabularies
  • Download your annotated JSON data dictionary
    • What next?

    - You can now use the new data dictionary to create a harmonized representation of your subject-level data (optional, uses other neurobagel tools).
    + You can now use the new data dictionary to create a harmonized representation of your subject-level data (optional, uses other neurobagel tools).
    To learn more about neurobagel, check out our website: neurobagel.org.

    @@ -71,6 +74,18 @@

    {{ uiText.dataDictionaryHeader }}

    + + Cannot reuse annotations + + +
    + At the moment, the annotation tool is not able to load previously created annotations. + This means that if you provide a data dictionary here that you created with Neurobagel, + any existing semantic annotations will be removed when the data dictionary is loaded. + + In practice this means that you cannot resume an aborted previous annotation. + This is a limitation we are going to address: #601. +     { + delete userDataDictionary[key].Annotations; + }); + + commit("setDataDictionary", { newDataDictionary: userDataDictionary, storeColumns: getters.getColumnNames }); commit("setDataDictionaryFilename", filename); }, From c49b1adf01136f30079fb9f02bcc16841749803b Mon Sep 17 00:00:00 2001 From: Sebastian Urchs Date: Thu, 18 Apr 2024 13:03:46 -0400 Subject: [PATCH 12/16] [MNT] Add plausible (#721) --- nuxt.config.js | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/nuxt.config.js b/nuxt.config.js index 5a26f240..04a9af8f 100644 --- a/nuxt.config.js +++ b/nuxt.config.js @@ -22,6 +22,12 @@ export default { script: [ { src: 'https://w.appzi.io/w.js?token=YVTHd' + }, + { + src: 'https://plausible.neurobagel.org/js/script.js', + 'data-domain': 'annotate.neurobagel.org', + async: 'async', + defer: 'defer' } ], htmlAttrs: { From 42b9ba10f8246b40f775f5ab5865473858ca3e97 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Apr 2024 23:28:29 -0400 Subject: [PATCH 13/16] Bump peaceiris/actions-gh-pages from 3 to 4 (#720) Bumps [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) from 3 to 4. - [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) - [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) - [Commits](https://github.com/peaceiris/actions-gh-pages/compare/v3...v4) --- updated-dependencies: - dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/cd.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cd.yaml b/.github/workflows/cd.yaml index f3a0d93b..ba82e53d 100644 --- a/.github/workflows/cd.yaml +++ b/.github/workflows/cd.yaml @@ -25,7 +25,7 @@ jobs: run: yarn generate - name: Deploy - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./dist From 6889666bdf1aac8c6f1e0b8f4f011dffec49e493 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Apr 2024 09:30:42 -0400 Subject: [PATCH 14/16] Bump eslint-plugin-vue from 9.24.1 to 9.25.0 (#718) --- package-lock.json | 14 +++++++------- package.json | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/package-lock.json b/package-lock.json index fe9e8f78..1a977953 100644 --- a/package-lock.json +++ b/package-lock.json @@ -30,7 +30,7 @@ "eslint": "^8.56.0", "eslint-config-airbnb": "^19.0.4", "eslint-plugin-cypress": "^2.15.1", - "eslint-plugin-vue": "^9.24.1", + "eslint-plugin-vue": "^9.25.0", "husky": "^9.0.11", "lint-staged": "^15.2.2", "push-dir": "^0.4.1" @@ -8109,9 +8109,9 @@ } }, "node_modules/eslint-plugin-vue": { - "version": "9.24.1", - "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.24.1.tgz", - "integrity": "sha512-wk3SuwmS1pZdcuJlokGYEi/buDOwD6KltvhIZyOnpJ/378dcQ4zchu9PAMbbLAaydCz1iYc5AozszcOOgZIIOg==", + "version": "9.25.0", + "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.25.0.tgz", + "integrity": "sha512-tDWlx14bVe6Bs+Nnh3IGrD+hb11kf2nukfm6jLsmJIhmiRQ1SUaksvwY9U5MvPB0pcrg0QK0xapQkfITs3RKOA==", "dev": true, "dependencies": { "@eslint-community/eslint-utils": "^4.4.0", @@ -25029,9 +25029,9 @@ "requires": {} }, "eslint-plugin-vue": { - "version": "9.24.1", - "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.24.1.tgz", - "integrity": "sha512-wk3SuwmS1pZdcuJlokGYEi/buDOwD6KltvhIZyOnpJ/378dcQ4zchu9PAMbbLAaydCz1iYc5AozszcOOgZIIOg==", + "version": "9.25.0", + "resolved": "https://registry.npmjs.org/eslint-plugin-vue/-/eslint-plugin-vue-9.25.0.tgz", + "integrity": "sha512-tDWlx14bVe6Bs+Nnh3IGrD+hb11kf2nukfm6jLsmJIhmiRQ1SUaksvwY9U5MvPB0pcrg0QK0xapQkfITs3RKOA==", "dev": true, "requires": { "@eslint-community/eslint-utils": "^4.4.0", diff --git a/package.json b/package.json index 99aa5910..b23db7a5 100644 --- a/package.json +++ b/package.json @@ -37,7 +37,7 @@ "eslint": "^8.56.0", "eslint-config-airbnb": "^19.0.4", "eslint-plugin-cypress": "^2.15.1", - "eslint-plugin-vue": "^9.24.1", + "eslint-plugin-vue": "^9.25.0", "husky": "^9.0.11", "lint-staged": "^15.2.2", "push-dir": "^0.4.1" From 7e5c44d51b0ca38429da3a035d8b934bb29d610c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Apr 2024 09:31:17 -0400 Subject: [PATCH 15/16] Bump cypress from 13.6.3 to 13.8.0 (#722) --- package-lock.json | 22 +++++++++++----------- package.json | 2 +- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1a977953..3a21730f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -25,7 +25,7 @@ }, "devDependencies": { "cy-verify-downloads": "^0.2.3", - "cypress": "^13.6.3", + "cypress": "^13.8.0", "editorconfig": "^2.0.0", "eslint": "^8.56.0", "eslint-config-airbnb": "^19.0.4", @@ -6854,9 +6854,9 @@ "integrity": "sha1-WW6WmP0MgOEgOMK4LW6xs1tiJNk=" }, "node_modules/cypress": { - "version": "13.6.3", - "resolved": "https://registry.npmjs.org/cypress/-/cypress-13.6.3.tgz", - "integrity": "sha512-d/pZvgwjAyZsoyJ3FOsJT5lDsqnxQ/clMqnNc++rkHjbkkiF2h9s0JsZSyyH4QXhVFW3zPFg82jD25roFLOdZA==", + "version": "13.8.0", + "resolved": "https://registry.npmjs.org/cypress/-/cypress-13.8.0.tgz", + "integrity": "sha512-Qau//mtrwEGOU9cn2YjavECKyDUwBh8J2tit+y9s1wsv6C3BX+rlv6I9afmQnL8PmEEzJ6be7nppMHacFzZkTw==", "dev": true, "hasInstallScript": true, "dependencies": { @@ -6867,7 +6867,7 @@ "arch": "^2.2.0", "blob-util": "^2.0.2", "bluebird": "^3.7.2", - "buffer": "^5.6.0", + "buffer": "^5.7.1", "cachedir": "^2.3.0", "chalk": "^4.1.0", "check-more-types": "^2.24.0", @@ -6885,7 +6885,7 @@ "figures": "^3.2.0", "fs-extra": "^9.1.0", "getos": "^3.2.1", - "is-ci": "^3.0.0", + "is-ci": "^3.0.1", "is-installed-globally": "~0.4.0", "lazy-ass": "^1.6.0", "listr2": "^3.8.3", @@ -23937,9 +23937,9 @@ "integrity": "sha1-WW6WmP0MgOEgOMK4LW6xs1tiJNk=" }, "cypress": { - "version": "13.6.3", - "resolved": "https://registry.npmjs.org/cypress/-/cypress-13.6.3.tgz", - "integrity": "sha512-d/pZvgwjAyZsoyJ3FOsJT5lDsqnxQ/clMqnNc++rkHjbkkiF2h9s0JsZSyyH4QXhVFW3zPFg82jD25roFLOdZA==", + "version": "13.8.0", + "resolved": "https://registry.npmjs.org/cypress/-/cypress-13.8.0.tgz", + "integrity": "sha512-Qau//mtrwEGOU9cn2YjavECKyDUwBh8J2tit+y9s1wsv6C3BX+rlv6I9afmQnL8PmEEzJ6be7nppMHacFzZkTw==", "dev": true, "requires": { "@cypress/request": "^3.0.0", @@ -23949,7 +23949,7 @@ "arch": "^2.2.0", "blob-util": "^2.0.2", "bluebird": "^3.7.2", - "buffer": "^5.6.0", + "buffer": "^5.7.1", "cachedir": "^2.3.0", "chalk": "^4.1.0", "check-more-types": "^2.24.0", @@ -23967,7 +23967,7 @@ "figures": "^3.2.0", "fs-extra": "^9.1.0", "getos": "^3.2.1", - "is-ci": "^3.0.0", + "is-ci": "^3.0.1", "is-installed-globally": "~0.4.0", "lazy-ass": "^1.6.0", "listr2": "^3.8.3", diff --git a/package.json b/package.json index b23db7a5..01ea4f6e 100644 --- a/package.json +++ b/package.json @@ -32,7 +32,7 @@ }, "devDependencies": { "cy-verify-downloads": "^0.2.3", - "cypress": "^13.6.3", + "cypress": "^13.8.0", "editorconfig": "^2.0.0", "eslint": "^8.56.0", "eslint-config-airbnb": "^19.0.4", From 805e6e15083d4036742e253f5477660851abfd7a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Apr 2024 11:51:15 -0400 Subject: [PATCH 16/16] Bump vue-select from 3.20.2 to 3.20.3 (#719) Bumps [vue-select](https://github.com/sagalbot/vue-select) from 3.20.2 to 3.20.3. - [Release notes](https://github.com/sagalbot/vue-select/releases) - [Changelog](https://github.com/sagalbot/vue-select/blob/master/release.config.js) - [Commits](https://github.com/sagalbot/vue-select/compare/v3.20.2...v3.20.3) --- updated-dependencies: - dependency-name: vue-select dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- package-lock.json | 14 +++++++------- package.json | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/package-lock.json b/package-lock.json index 3a21730f..92c91397 100644 --- a/package-lock.json +++ b/package-lock.json @@ -18,7 +18,7 @@ "nuxt": "^2.17.3", "papaparse": "^5.4.1", "vue": "^2.7.16", - "vue-select": "^3.20.2", + "vue-select": "^3.20.3", "vue-server-renderer": "^2.7.16", "vue-template-compiler": "^2.7.16", "webpack": "^4.47.0" @@ -17949,9 +17949,9 @@ "integrity": "sha512-VYXZQLtjuvKxxcshuRAwjHnciqZVoXAjTjcqBTz4rKc8qih9g9pI3hbDjmqXaHdgL3v8pV6P8Z335XvHzESxLQ==" }, "node_modules/vue-select": { - "version": "3.20.2", - "resolved": "https://registry.npmjs.org/vue-select/-/vue-select-3.20.2.tgz", - "integrity": "sha512-ZSzIDzyYsWZULGUxVp1h6u3yi9IZQBWX8r6kSudUI/I5J1HQKpBjRntvkrg6pr87xmm16kdChvHCDN+W84vTKw==", + "version": "3.20.3", + "resolved": "https://registry.npmjs.org/vue-select/-/vue-select-3.20.3.tgz", + "integrity": "sha512-aDaq4rPBrDavh7NDLgAP8e0G8UNElh6vO3itGWjhf1y9KaGRWtFw21cUkSRHGgj0V5FlCG4EaRb1xdE/C9J+eg==", "peerDependencies": { "vue": "2.x" } @@ -31946,9 +31946,9 @@ "integrity": "sha512-VYXZQLtjuvKxxcshuRAwjHnciqZVoXAjTjcqBTz4rKc8qih9g9pI3hbDjmqXaHdgL3v8pV6P8Z335XvHzESxLQ==" }, "vue-select": { - "version": "3.20.2", - "resolved": "https://registry.npmjs.org/vue-select/-/vue-select-3.20.2.tgz", - "integrity": "sha512-ZSzIDzyYsWZULGUxVp1h6u3yi9IZQBWX8r6kSudUI/I5J1HQKpBjRntvkrg6pr87xmm16kdChvHCDN+W84vTKw==", + "version": "3.20.3", + "resolved": "https://registry.npmjs.org/vue-select/-/vue-select-3.20.3.tgz", + "integrity": "sha512-aDaq4rPBrDavh7NDLgAP8e0G8UNElh6vO3itGWjhf1y9KaGRWtFw21cUkSRHGgj0V5FlCG4EaRb1xdE/C9J+eg==", "requires": {} }, "vue-server-renderer": { diff --git a/package.json b/package.json index 01ea4f6e..ad59b67b 100644 --- a/package.json +++ b/package.json @@ -25,7 +25,7 @@ "nuxt": "^2.17.3", "papaparse": "^5.4.1", "vue": "^2.7.16", - "vue-select": "^3.20.2", + "vue-select": "^3.20.3", "vue-server-renderer": "^2.7.16", "vue-template-compiler": "^2.7.16", "webpack": "^4.47.0"